Re^2: list lines not found in config (while+if)

Taking your sample data and original code I've generated the following sample code. Note that I added strictures and cleaned up a few other aspects of you code. I also removed the first line of your reference file so that at least one "missing" line would be reported.

use strict;
use warnings;

my $File1 = <<END_FILE1;
GP_MASA_38C02_c
GP_MASA_33B06_c
GP_MASA_24D04_c
GP_MASA_35A04_c
END_FILE1

my $File2 = <<END_FILE2;
'GP_MASA_01F04_c',681,'ACCACACATCATCTGACTTACGTACGTACG......
'GP_MASA_38C02_c',273,'ACATCCTTCACAGAAGTTTGT.............
'GP_MASA_33B06_c',288,'ACATACTAACACGGTCTTT...............
END_FILE2

my $match = 0;

open my $dataIn, '<', \$File2;

while (<$dataIn>) {
    chomp ($_);
    my $dataLine = $_;

    open my $refIn, '<', \$File1;

    while (<$refIn>) {
        chomp ($_);
        my $str = $_;
        if ($dataLine =~ /$str/) {
            $match = 1;
        }
    }
    close ($refIn);
    if ($match == 0) {
        print "$dataLine\n";

    }
    $match = 0;
}
[download]

Prints:

'GP_MASA_01F04_c',681,'ACCACACATCATCTGACTTACGTACGTACG......
[download]

Although reparsing the reference file for each line of the data file is exceedingly nasty, the code works. Maybe you can update the sample to demonstrate where you are seeing a problem?

True laziness is hard work

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Re^3: list lines not found in config (while+if) by tangledupinperl (Initiate) on Apr 08, 2009 at 11:19 UTC
Ive gone through and put print's throughout the script and ive finaly found out the problem! its the bloody matching string. there is something in my reference file that matching each time it reads the data file i did a: `if($s_line =~ /$str/){ print "$str -- match\n"; } else { print "$str -- no match\n"; }` [download] on my test data and it shown that its matching an empty line so there must be something in my reference file thats matching up (ive already checked and its not empty lines). I'm gonna look for it now so i wont keep you hanging on, but cheers for all the improvement suggestions. Im going to go through them all when I have more time and no deadline to catch cheers for the help! in heinsight, I should have given better examples at the start. sorry. will do next time	[reply] [d/l]

Replies are listed 'Best First'.

Re^3: list lines not found in config (while+if)
by tangledupinperl (Initiate) on Apr 08, 2009 at 11:19 UTC

 if($s_line =~ /$str/){
    print "$str -- match\n";
    } else {
    print "$str -- no match\n";
    }
[download]

[reply]
[d/l]